[phenixbb] Jumping Rfree upon bulk solvent modeling
Pavel Afonine
pafonine at lbl.gov
Tue Jan 8 10:21:03 PST 2019
Hi Tobias,
> Dear PHENIXBB community,
>
> i have come across a strange behavior in Phenix:
>
> * I copied Rfree-flags from a dataset with very slightly different
> unit cell
>
> * Refined the previously refined model against the new data
>
> * Rfactors in first round were good
>
> * Second round in refinement Rfree was up by 10 % just from the
> start during bulk solvent modeling and scaling
>
> * In another round Rfree was high in the beginning, and then dropped
> by those 10 % during bulk solvent modelling and scaling.
>
> * In yet another round Rfree started 10% lower than the previous
> round during bulk solvent modeling in the first cycle and then it
> jumps up again in the second cycle.
>
> What could be wrong?
>
If I take a random structure from PDB:
phenix.fetch_pdb 1f8t --mtz
and run a default phenix.refine job:
phenix.refine 1f8t.{pdb,mtz}
then look at the log file, I see:
For the first macro-cycle:
(...)
start: r(all,work,free)=0.3064 0.3018 0.3435
n_refl.: 27466
re-set all scales: r(all,work,free)=0.3064 0.3018 0.3435
n_refl.: 27466
remove outliers: r(all,work,free)=0.3061 0.3016 0.3435
n_refl.: 27464
overall B=0.38 to atoms: r(all,work,free)=0.3096 0.3050 0.3470
n_refl.: 27464
bulk-solvent and scaling: r(all,work,free)=0.1839 0.1798 0.2213 n_refl.:
27464
remove outliers: r(all,work,free)=0.1839 0.1798 0.2213
n_refl.: 27464
(..)
Here:
- "start" means no any solvent modeling and scaling was yet done;
- last line shows R values after all corrections.
Now, for the second macro-cycle we see:
()
start: r(all,work,free)=0.1798 0.1754 0.2195
n_refl.: 27464
re-set all scales: r(all,work,free)=0.3200 0.3151 0.3607
n_refl.: 27464
remove outliers: r(all,work,free)=0.3200 0.3151 0.3607
n_refl.: 27464
overall B=-2.56 to atoms: r(all,work,free)=0.2961 0.2912 0.3366 n_refl.:
27464
bulk-solvent and scaling: r(all,work,free)=0.1783 0.1739 0.2183 n_refl.:
27464
remove outliers: r(all,work,free)=0.1783 0.1739 0.2183
n_refl.: 27464
()
Here, "start" shows values obtained by the end of 1st macro-cycle,
second line (re-set all scale) shows values after all scales were
discarded, and the last line shows values R values after all scales were
re-calculated again.
So.. if this is what you observe, then there is nothing wrong.
Otherwise, please send me the log file and I will have a closer look.
Pavel
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